Alignments for a candidate for L-LDH in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for L-LDH in Klebsiella michiganensis M5al

Align L-lactate dehydrogenase 1; L-LDH 1; EC 1.1.1.27 (characterized)
to candidate BWI76_RS15220 BWI76_RS15220 L-lactate dehydrogenase

Query= SwissProt::A6QDL6
         (317 letters)



>FitnessBrowser__Koxy:BWI76_RS15220
          Length = 314

 Score =  251 bits (640), Expect = 2e-71
 Identities = 124/308 (40%), Positives = 190/308 (61%), Gaps = 1/308 (0%)

Query: 5   KGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRV 64
           K  KV++IG G VG+S A++L+NQS+ +EL+++DL+  +      DL  A  Y P  + +
Sbjct: 4   KARKVMIIGAGNVGASAAYALLNQSVCEELILVDLNKPRAEAHAQDLSDAAAYMPGMMTI 63

Query: 65  KAGEYSDCHDADLVVIC-AGAAQKPGETRLDLVSKNLKIFKSIVGEVMASKFDGIFLVAT 123
              E SDC D D+ VI  +G A KPG+TRLD ++   KI KS+V ++M   F+GIFLVAT
Sbjct: 64  STREASDCADVDIAVITVSGGALKPGQTRLDELTNTAKIVKSLVPQMMNGGFNGIFLVAT 123

Query: 124 NPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTE 183
           NP DI+ +  W+ SGLP+ +V+G+G  LD+ R R +L++A D+  +S+DA I+GEHGD +
Sbjct: 124 NPCDIITWQVWQLSGLPRGQVLGTGVWLDTTRLRRVLAQALDIGAQSIDAFILGEHGDAQ 183

Query: 184 LPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARI 243
            PVWSH+ + G  +  + ++        + I  + R   ++I   KG T YGVA  +A I
Sbjct: 184 FPVWSHSAVYGSAIADVYQKHTGKALDRDLIADKVRKLGFEIYAGKGCTEYGVAGTIAEI 243

Query: 244 TEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSA 303
              IF      L VS +L+GEY       GVPAV+ ++G++ ++E+ L D+E  KF H+ 
Sbjct: 244 CRNIFTGSHRALAVSCILDGEYGVTGAAAGVPAVLTQSGVQQIIELQLADDEAEKFRHAI 303

Query: 304 KTLKDIMA 311
           + +K  +A
Sbjct: 304 EVIKASIA 311


Lambda     K      H
   0.317    0.135    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 265
Number of extensions: 7
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 317
Length of database: 314
Length adjustment: 27
Effective length of query: 290
Effective length of database: 287
Effective search space:    83230
Effective search space used:    83230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS15220 BWI76_RS15220 (L-lactate dehydrogenase)
to HMM TIGR01771 (L-lactate dehydrogenase (EC 1.1.1.27))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01771.hmm
# target sequence database:        /tmp/gapView.18401.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01771  [M=299]
Accession:   TIGR01771
Description: L-LDH-NAD: L-lactate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.5e-109  350.7   0.0   3.9e-109  350.5   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS15220  BWI76_RS15220 L-lactate dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS15220  BWI76_RS15220 L-lactate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.5   0.0  3.9e-109  3.9e-109       1     298 [.      10     307 ..      10     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 350.5 bits;  conditional E-value: 3.9e-109
                               TIGR01771   1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvvit 71 
                                             iiGag+VG+s+a+all+q++++el+l+D+n+ +ae++a dlsdaa++++  +++++++++d++d+d+ vit
  lcl|FitnessBrowser__Koxy:BWI76_RS15220  10 IIGAGNVGASAAYALLNQSVCEELILVDLNKPRAEAHAQDLSDAAAYMPGMMTISTREASDCADVDIAVIT 80 
                                             8********************************************************************** PP

                               TIGR01771  72 a.GaeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvL 141
                                             + G + kpg+tRl+++++++ki+ks+v+++++ gf+gi+lv++NP+Di+t  v++lsglp+ +v+G+G++L
  lcl|FitnessBrowser__Koxy:BWI76_RS15220  81 VsGGALKPGQTRLDELTNTAKIVKSLVPQMMNGGFNGIFLVATNPCDIITWQVWQLSGLPRGQVLGTGVWL 151
                                             845667***************************************************************** PP

                               TIGR01771 142 dtaRlrrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiekevrda 212
                                             dt+Rlrr+la++l++ ++s++a++lGEHGd++++vws+  + g  + ++ +++ + k  + + i ++vr+ 
  lcl|FitnessBrowser__Koxy:BWI76_RS15220 152 DTTRLRRVLAQALDIGAQSIDAFILGEHGDAQFPVWSHSAVYGSAIADVYQKH-TGKALDRDLIADKVRKL 221
                                             *************************************************9855.558888889******** PP

                               TIGR01771 213 ayeiiekKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLs 283
                                             ++ei+  Kg+T+yg++ ++a+i+++i++ ++r l vs++l+geyg+++ + gvPavl+++Gv++i+el+L 
  lcl|FitnessBrowser__Koxy:BWI76_RS15220 222 GFEIYAGKGCTEYGVAGTIAEICRNIFTGSHRALAVSCILDGEYGVTGAAAGVPAVLTQSGVQQIIELQLA 292
                                             *********************************************************************** PP

                               TIGR01771 284 eeEkeklkksaetlk 298
                                             ++E ek+++++e++k
  lcl|FitnessBrowser__Koxy:BWI76_RS15220 293 DDEAEKFRHAIEVIK 307
                                             ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (314 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.63
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources